The honeymoon seems to be ending between retired Gen. James N. Mattis and Donald Trump’s transition team amid an increasingly acrimonious dispute over who will get top jobs in the Defense Department — and who gets to make those decisions.

With only two weeks left before Inauguration Day and days before Mattis’s Senate confirmation hearing, most major Pentagon civilian positions remain unfilled. Behind the scenes, Mattis has been rejecting large numbers of candidates offered by the transition team for several top posts, two sources close to the transition said. The dispute over personnel appointments is contributing to a tenser relationship between Mattis and the transition officials, which could set the stage for turf wars between the Pentagon and the White House in the coming Trump administration.

The Trump transition team was already considering candidates for a host of Defense Department top jobs when Trump announced Dec. 1 that he intended to nominate “Mad Dog” Mattis to lead the military. The Mattis pick was seen by Republicans around Washington as an indication that Trump would rely on senior and experienced officials to shape and implement his national security and foreign policies. Many “Never Trump” Republicans also thought this might be their way into service despite having opposed Trump in the GOP primary.

Retired U.S. Marine Corps General James Mattis is President Trump's Secretary of Defense. Here's what you need to know about "Mad Dog Mattis." (Jenny Starrs/The Washington Post)

Initially, both Mattis and the Trump team intended to engage in a collaborative process whereby Mattis would be given significant influence and participation in selecting top Pentagon appointees.

But the arrangement started going south only two weeks later when Mattis had to learn from the news media that Trump had selected Vincent Viola, a billionaire Army veteran, to be secretary of the Army, one source close to the transition said.

“Mattis was furious,” said the source. “It made him suspicious of the transition team, and things devolved from there.”

Service secretaries represent potential alternate power centers inside the Defense Department, and Mattis as defense secretary has an interest in having secretaries who are loyal to him and don’t have independent relationships with the White House.

Mattis is also pushing for the Trump transition team to allow “Never Trump” Republicans to serve in the Pentagon, but so far the Trump team is refusing.

One position that is a source of tension is undersecretary of defense for intelligence, a powerful post that oversees all Defense Department intelligence agencies, which include the National Security Agency and the Defense Intelligence Agency.

Retired Lt. Gen. Michael T. Flynn, President-elect Trump’s national security adviser-designate, was DIA director until he was sacked by Director of National Intelligence James R. Clapper Jr. following a dispute with then-Undersecretary of Defense for Intelligence Michael G. Vickers.

Mattis has rejected all of the names the Trump team has offered to be the top intelligence official in the department, another transition source said. Mattis is also unlikely to accept Trump’s top Pentagon transition landing team official, Mira Ricardel, as a top official. She was rumored to be in line to be undersecretary of defense for policy, a hugely influential job.

“Let’s put it this way, he’s being very picky about the options presented to him,” said the source, who was not authorized to talk about internal deliberations.

Transition sources also said that David McCormick, a hedge fund manager and former Army officer, is still Trump’s likely pick to be deputy defense secretary, the No. 2 job under Mattis.

The personnel dispute could be the first sign of tension between Mattis and Flynn. As a four-star general and head of Central Command, Mattis outranked Flynn when Flynn was DIA director, a three-star position. If confirmed, Mattis would be a Cabinet member and a member of the president’s National Security Council, but Flynn has a close relationship with Trump and the duty of coordinating between all the national security agencies.

The Trump transition team did not respond to a request for comment.

Meanwhile, Flynn is busily filling up the National Security Council staff with military and intelligence officers he knows personally. For example, as the Nelson Report first reported, Flynn intends to make Matthew Pottinger the senior director for Asia on the NSC staff.

Pottinger, a former Wall Street Journal reporter in China, joined the Marines in 2005. While deployed in Afghanistan as an intelligence officer, he worked closely with Flynn and co-authored a memo on how to fix intelligence operations in Afghanistan that was later released by a Washington think tank in 2010.

Flynn has also been meeting foreign officials, especially from Europe, with Sebastian Gorka, a professor and vice president of the Institute of World Politics, who was born in Britain to parents who fled Hungary. What position Gorka will have in Flynn’s NSC staff is unclear. Both Pottinger and Gorka are well-respected but their new prominence has raised concerns that Flynn is placing too much emphasis on military officials and military experts, in effect militarizing the NSC staff.

K.T. McFarland, who is set to be Flynn’s top deputy, is pushing for more civilian and policy-focused NSC staff appointments, transition sources said.

Several Washington foreign policy experts who are in touch with the Trump transition team said that overall, there’s no uniformity in the way each department is being handled and no real understanding of how much autonomy each Cabinet member will have in running his or her agency.

Many expect the agencies to have more power than usual because the Trump team is planning to slash the NSC staff from more than 400 people to about 150 personnel. Then again, national security officials outside the White House may find it difficult to exert influence with a president who often alters major policies by tweet.

Some chaos and turf battles are to be expected in any presidential transition but the Trump team is off to a bad start. Trump often touts his talent in selecting good people. If he wants to keep those people happy, he should work to settle their disputes and address their grievances before they get out of hand.

UPDATE: The Trump transition team emailed me this statement: “We are ahead of schedule with assembling the most qualified cabinet and administration in history. Any implication contrary to that is completely false and from sources who do not have any knowledge of our transition efforts.”

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Here’s a look at Trump’s administration so far

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The men and women the president-elect has selected for his Cabinet and White House team.

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The men and women the president-elect has selected for his Cabinet and White House team.

Scott Gottlieb, nominee for commissioner of FDAPresident Trump is set to nominate Scott Gottlieb, a conservative physician and businessman with deep ties to the pharmaceutical industry, to be commissioner of the Food and Drug Administration, a White House official said.Courtesy of American Enterprise Institute/via Reuters